X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makefile;h=163db6bd0c547f2b73055ab5b4498dbd82ebfea3;hp=7cc71f0e9a4064a2163707f3f7bc08da36af2b5e;hb=615301e57c25e241356a9c2380648d117709458d;hpb=095a4c7aed0cf5ef79eaf28f0d79d3aa51c2811e

diff --git a/makefile b/makefile
index 7cc71f0..163db6b 100644
--- a/makefile
+++ b/makefile
@@ -14,12 +14,14 @@ USEMPI ?= no
 USEREADLINE ?= yes
 CYGWIN_BUILD ?= no
 USECOMPRESSION ?= no
-MOTHUR_FILES = "\"../release\""
-RELEASE_DATE = "\"2/7/2011\""
-VERSION = "\"1.16.0\""
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"5/29/2013\""
+VERSION = "\"1.31.1\""
+FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS = 
 
 # Optimize to level 3:
-CXXFLAGS += -O3
+CXXFLAGS += -O3 
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#if you are using centos uncomment the following lines
@@ -28,10 +30,17 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#if you are a mac user use the following line
 	TARGET_ARCH += -arch x86_64
 	
+	#if you using cygwin to build Windows the following line
+	#CXX = x86_64-w64-mingw32-g++
+	#CC = x86_64-w64-mingw32-g++
+	#FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
+ 	#TARGET_ARCH += -m64 -static
+
 	#if you are a linux user use the following line
 	#CXXFLAGS += -mtune=native -march=native -m64
 	
-	 CXXFLAGS += -DBIT_VERSION
+	CXXFLAGS += -DBIT_VERSION 
+    FORTRAN_FLAGS = -m64
 endif
 
 
@@ -84,11 +93,18 @@ endif
 
 OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
 OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
 
-mothur : $(OBJECTS)
+mothur : fortranSource $(OBJECTS) uchime
 	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
 	
 	strip mothur
+ 
+uchime:
+	cd uchime_src && ./mk && mv uchime .. && cd ..
+	
+fortranSource:
+	${FORTAN_COMPILER} -c $(FORTRAN_FLAGS) *.f
 
 install : mothur
 #	cp mothur ../Release/mothur
@@ -103,4 +119,5 @@ install : mothur
 
 clean :
 	@rm -f $(OBJECTS)
+	@rm -f uchime